COVID-19 trajectories among 57 million adults in England: a cohort study using electronic health records
Authors: Johan H Thygesen, Christopher Tomlinson, Sam Hollings, Mehrdad A Mizani, Alex Handy, Ashley Akbari, Amitava Banerjee, Jennifer Cooper, Alvina G Lai, Kezhi Li, Bilal A Mateen, Naveed Sattar, Reecha Sofat, Ana Torralbo, Honghan Wu, Angela Wood, Jonathan A C Sterne, Christina Pagel, William N Whiteley, Cathie Sudlow, Harry Hemingway, Spiros Denaxas, Hoda Abbasizanjani, Nida Ahmed, Badar Ahmed, Ashley Akbari, Abdul Qadr Akinoso-Imran, Elias Allara, Freya Allery, Emanuele Di Angelantonio, Mark Ashworth, Vandana Ayyar-Gupta, Sonya Babu-Narayan, Seb Bacon, Steve Ball, Ami Banerjee, Mark Barber, Jessica Barrett, Marion Bennie, Colin Berry, Jennifer Beveridge, Ewan Birney, Lana Bojanić, Thomas Bolton, Anna Bone, Jon Boyle, Tasanee Braithwaite, Ben Bray, Norman Briffa, David Brind, Katherine Brown, Maya Buch, Dexter Canoy, Massimo Caputo, Raymond Carragher, Alan Carson, Genevieve Cezard, Jen-Yu Amy Chang, Kate Cheema, Richard Chin, Yogini Chudasama, Jennifer Cooper, Emma Copland, Rebecca Crallan, Rachel Cripps, David Cromwell, Vasa Curcin, Gwenetta Curry, Caroline Dale, John Danesh, Jayati Das-Munshi, Ashkan Dashtban, Alun Davies, Joanna Davies, Gareth Davies, Neil Davies, Joshua Day, Antonella Delmestri, Spiros Denaxas, Rachel Denholm, John Dennis, Alastair Denniston, Salil Deo, Baljean Dhillon, Annemarie Docherty, Tim Dong, Abdel Douiri, Johnny Downs, Alexandru Dregan, Elizabeth A Ellins, Martha Elwenspoek, Fabian Falck, Florian Falter, Yat Yi Fan, Joseph Firth, Lorna Fraser, Rocco Friebel, Amir Gavrieli, Moritz Gerstung, Ruth Gilbert, Clare Gillies, Myer Glickman, Ben Goldacre, Raph Goldacre, Felix Greaves, Mark Green, Luca Grieco, Rowena Griffiths, Deepti Gurdasani, Julian Halcox, Nick Hall, Tuankasfee Hama, Alex Handy, Anna Hansell, Pia Hardelid, Flavien Hardy, Daniel Harris, Camille Harrison, Katie Harron, Abdelaali Hassaine, Lamiece Hassan, Russell Healey, Harry Hemingway, Angela Henderson, Naomi Herz, Johannes Heyl, Mira Hidajat, Irene Higginson, Rosie Hinchliffe, Julia Hippisley-Cox, Frederick Ho, Mevhibe Hocaoglu, Sam Hollings, Elsie Horne, David Hughes, Ben Humberstone, Mike Inouye, Samantha Ip, Nazrul Islam, Caroline Jackson, David Jenkins, Xiyun Jiang, Shane Johnson, Umesh Kadam, Costas Kallis, Zainab Karim, Jake Kasan, Michalis Katsoulis, Kim Kavanagh, Frank Kee, Spencer Keene, Seamus Kent, Sara Khalid, Anthony Khawaja, Kamlesh Khunti, Richard Killick, Deborah Kinnear, Rochelle Knight, Ruwanthi Kolamunnage-Dona, Evan Kontopantelis, Amanj Kurdi, Ben Lacey, Alvina Lai, Andrew Lambarth, Milad Nazarzadeh Larzjan, Deborah Lawler, Thomas Lawrence, Claire Lawson, Qiuju Li, Ken Li, Miguel Bernabeu Llinares, Paula Lorgelly, Deborah Lowe, Jane Lyons, Ronan Lyons, Pedro Machado, Mary Joan Macleod, John Macleod, Evaleen Malgapo, Mamas Mamas, Mohammad Mamouei, Sinduja Manohar, Rutendo Mapeta, Javiera Leniz Martelli, David Moreno Martos, Bilal Mateen, Aoife McCarthy, Craig Melville, Rebecca Milton, Mehrdad Mizani, Marta Pineda Moncusi, Daniel Morales, Ify Mordi, Lynn Morrice, Carole Morris, Eva Morris, Yi Mu, Tanja Mueller, Lars Murdock, Vahé Nafilyan, George Nicholson, Elena Nikiphorou, John Nolan, Tom Norris, Ruth Norris, Laura North, Teri-Louise North, Dan O'Connell, Dominic Oliver, Adejoke Oluyase, Abraham Olvera-Barrios, Efosa Omigie, Sarah Onida, Sandosh Padmanabhan, Tom Palmer, Laura Pasea, Riyaz Patel, Rupert Payne, Jill Pell, Carmen Petitjean, Arun Pherwani, Owen Pickrell, Livia Pierotti, Munir Pirmohamed, Rouven Priedon, Dani Prieto-Alhambra, Alastair Proudfoot, Terry Quinn, Jennifer Quint, Elena Raffetti, Kazem Rahimi, Shishir Rao, Cameron Razieh, Brian Roberts, Caroline Rogers, Jennifer Rossdale, Safa Salim, Nilesh Samani, Naveed Sattar, Christian Schnier, Roy Schwartz, David Selby, Olena Seminog, Sharmin Shabnam, Ajay Shah, Jon Shelton, James Sheppard, Shubhra Sinha, Mirek Skrypak, Martina Slapkova, Katherine Sleeman, Craig Smith, Reecha Sofat, Filip Sosenko, Matthew Sperrin, Sarah Steeg, Jonathan Sterne, Serban Stoica, Maria Sudell, Cathie Sudlow, Luanluan Sun, Arun Karthikeyan Suseeladevi, Michael Sweeting, Matt Sydes, Rohan Takhar, Howard Tang, Johan Thygesen, George Tilston, Claire Tochel, Clea du Toit, Christopher Tomlinson, Renin Toms, Fatemeh Torabi, Ana Torralbo, Julia Townson, Adnan Tufail, Tapiwa Tungamirai, Susheel Varma, Sebastian Vollmer, Venexia Walker, Tianxiao Wang, Huan Wang, Alasdair Warwick, Ruth Watkinson, Harry Watson, William Whiteley, Hannah Whittaker, Harry Wilde, Tim Wilkinson, Gareth Williams, Michelle Williams, Richard Williams, Eloise Withnell, Charles Wolfe, Angela Wood, Lucy Wright, Honghan Wu, Jinge Wu, Jianhua Wu, Tom Yates, Francesco Zaccardi, Haoting Zhang, Huayu Zhang, Luisa Zuccolo
Journal: The Lancet Digital Health (2022)

BackgroundUpdatable estimates of COVID-19 onset, progression, and trajectories underpin pandemic mitigation efforts. To identify and characterise disease trajectories, we aimed to define and validate ten COVID-19 phenotypes from nationwide linked electronic health records (EHR) using an extensible framework.MethodsIn this cohort study, we used eight linked National Health Service (NHS) datasets for people in England alive on Jan 23, 2020. Data on COVID-19 testing, vaccination, primary and secondary care records, and death registrations were collected until Nov 30, 2021. We defined ten COVID-19 phenotypes reflecting clinically relevant stages of disease severity and encompassing five categories: positive SARS-CoV-2 test, primary care diagnosis, hospital admission, ventilation modality (four phenotypes), and death (three phenotypes). We constructed patient trajectories illustrating transition frequency and duration between phenotypes. Analyses were stratified by pandemic waves and vaccination status.FindingsAmong 57 032 174 individuals included in the cohort, 13 990 423 COVID-19 events were identified in 7 244 925 individuals, equating to an infection rate of 12·7% during the study period. Of 7 244 925 individuals, 460 737 (6·4%) were admitted to hospital and 158 020 (2·2%) died. Of 460 737 individuals who were admitted to hospital, 48 847 (10·6%) were admitted to the intensive care unit (ICU), 69 090 (15·0%) received non-invasive ventilation, and 25 928 (5·6%) received invasive ventilation. Among 384 135 patients who were admitted to hospital but did not require ventilation, mortality was higher in wave 1 (23 485 [30·4%] of 77 202 patients) than wave 2 (44 220 [23·1%] of 191 528 patients), but remained unchanged for patients admitted to the ICU. Mortality was highest among patients who received ventilatory support outside of the ICU in wave 1 (2569 [50·7%] of 5063 patients). 15 486 (9·8%) of 158 020 COVID-19-related deaths occurred within 28 days of the first COVID-19 event without a COVID-19 diagnoses on the death certificate. 10 884 (6·9%) of 158 020 deaths were identified exclusively from mortality data with no previous COVID-19 phenotype recorded. We observed longer patient trajectories in wave 2 than wave 1.InterpretationOur analyses illustrate the wide spectrum of disease trajectories as shown by differences in incidence, survival, and clinical pathways. We have provided a modular analytical framework that can be used to monitor the impact of the pandemic and generate evidence of clinical and policy relevance using multiple EHR sources.FundingBritish Heart Foundation Data Science Centre, led by Health Data Research UK.